The analysis of an ionic profile of exhaled breath condensate (EBC) by capillary electrophoresis with contactless conductivity detection and double opposite end injection, is demonstrated. A miniature sampler made from a 2 ml syringe and an aluminium cooling cylinder was used for the fast collection of EBC (under one minute). Analysis of the collected EBC was performed in a 60 mM 2-(N-morpholino)ethanesulfonic acid, 60 mM L-histidine background electrolyte with 30 µM cetyltrimethylammonium bromide and 2 mM 18-crown-6 at pH 6, and excellent repeatability of migration times (RSD <1.3% (n = 7)) and peak areas (RSD < 7% (n = 7)) of 14 ions (inorganic anions, cations and organic acids) was obtained. It is demonstrated that the analysis of EBC samples obtained from patients with various respiratory diseases (chronic obstructive pulmonary disease, asthma, pulmonary fibrosis, sarcoidosis, cystic fibrosis) is possible in less than five minutes and the ionic profile can be compared with the group of healthy individuals. The analysis of the ionic profile of EBC samples provides a set of data in which statistically significant differences among the groups of patients could be observed for several clinically relevant anions (nitrite, nitrate, acetate, lactate). The developed collection system and method provides a highly reproducible and fast way of collecting and analyzing EBC, with future applicability in point-of-care diagnostics.